Scripts

Revision as of 11:01, 9 April 2011

Here we describe the various scripts we are using for the NGC 1333 project. Most of them will be based on the Miriad package, but we will also be using DS9, KARMA and NEMO. To simplify/organize our scripts, we have assembled a CVS module called MIS, in which all scripts (and default parameter data to run the scripts) are maintained. First we describe MIS, after that the individual scripts.

MIS (Miriad Interferometry Singledish) toolkit

This is our CVS based module to organize all our reduction scripts and store the parameters important for them as well. We separate these in a script independant way, so we allow anybody to use csh, sh, python, fortran, C, C++, Java, ...... There is also a manual available, although you can also generate a new one from your own MIS version.

If you want to grab a copy of MIS, for now use our CVS repository version (or use this tar file which you will need to cvs update):

 cvs -d :pserver:$USER@cvs.astro.umd.edu:/home/cvsroot checkout mis

where $USER is your given username in CVS (or use anonymous.

If you have never used CVS before, get your introduction from our CARMA pages here. If you need an account, you will need to email Peter your preferred username, and the hashed output of the password generator (details in that link) via the command

  perl -e 'print crypt("my_password","b6"), "\n";' 

and he better not get the response b60j72OwWnjlk from you!!!

Once you have obtained MIS, get it ready for installation:

  cd mis
  ./configure
  source mis_start.csh

and you are in principle ready to use the MIS scripts. There are some additional powerful options to construct automated pipelines, but that is for another chapter.

Occasionally there will be updates. If you are not a developer, and just want to update MIS from what others have done, this should work in most cases:

  mis -u

whereas

  mis -i

is simply a shortcut to committing all your MIS changes back to CVS for others to pick up. Use that with caution, as it could commit more than you may have bargained for!

Scripts

Not all scripts have been properly MIS-pipelined yet! Keywords followed by = means they can be input in this script, keywords preceded by = means they are set by this script

• getdata: project= rawdata= ary= track= =cvis
• report:
• map_inttime: source= =np
• uvcatSD: offname= fix=
• reduceSD.csh: example of single dish data reduction (using sinbad/sinpoly/varmaps) - MWP
• do_reduceSD: the same script, but now MIStified as well as cleaned up.
• do_mapSD: creates the SD cubes
• do_uvcat1: cut interferometer size down to just the 4 USB windows, and apply flags
• do_inspect1: inspect your data (you can edit to suit your needs)
• do_cal1: calibrate
• do_mos1: example mosaicing of just the UV data
• lincomb.csh: template script for combination of singledish and interferometric data using mossdi ("Stanimirovic method").

Example Session using MIS

A simple non-pipelined session could be as follows:

  mis -q
  mkdir data10
  cd data10
  pipepar -c rawdata=/home/teuben/carma/work/n1333/rawdata
  getdata project=cx323.1E_89NGC133.17
  getdata track=22 ary=E
  report
  map_inttime 

A more advanced session making the inttime map would be to first construct a pipeline consisting of getdata and map_inttime for all projects, and then use the piperun command to execute this.

  piperun -c n1333.lis 'pipeline 2 getdata map_inttime > Pipefile; pipepar -c project=%s; pipe all'

In each project directory you will then have a xyt.tab file for the next stage. For example to get a listing of how many pointings each track had, use

  piperun n1333.lis pipepar -v project -v np

and here's how to then create the inttime maps,in various formats (miriad, fits):

  mk_map_inttime.csh */xyt.tab

When new data come in

When new data come in, and it has been placed in the rawdata directory, the following MIS command will get it into your local (and hopefully otherwise empty) directory:

  pipepar -c
  getdata trial=1 ary=D
  report

where the ary=D is actually the default and not needed. Also, this will make a symlink, if you really must have a copy, add the link=0 keyword.

After this you can cut it down to its basic USB win4 (9,11,13,15) selection using

  do_uvcat1

for interferometric, and

  do_uvcatSD

for single dish. Go ahead and inspect it the way you like, and create a mis.uvflag file with entries such as

 edge=2
 tsys=500.
 select=time(23:09:00.0,23:10:00.0),source(3c84)
 select=ant(7),time(00:00:00.0,00:25:00.0)
 select=ant(7) tsys=20.,100. 
 select=time(23:00:00.0,23:20:00.0),ant(16)
 select=time(00:00:00.0,00:15:00.0),ant(16)
 select=ant(17),win(2,3)

you can formally flag this in pipeline fashion using

 do_uvflag vis=uvdata

or

 do_uvflag vis=sddata

once you are happy with the flag file, save it:

 pipesave

and if this is a new project, you will have to add it to CVS for others to benefit:

 cd $MIS/def
 cvs add cx323.1D_89NGC133.1
 cvs add cx323.1D_89NGC133.1/mis.*
 cvs commit

anybody else now can retrieve these using the command

 pipesetup

in your data project directory. Any changes to these persistent pipe files needs to be done using CVS, or if you only have those files to worry about (and not code) you can use our shortcut

 mis -i

Using CVS will give us a well known tool to make sure we're all agreeing on the parameters and the flag file(s), and whatever else we decide to save on a project-by-project (trial really) basis.

For final combined mapping we'll have to create another project, since only one mis.def file can exist per project.

Single Dish Data Reduction

When new data comes in, here is the standard list of things to do to reduce the Single Dish data (regardless of whether the interformeter people have already flagged things or not):

 mis -u
 mkdir ExampleD1
 cd ExampleD1
 pipepar -c
 getdata trial=1 ary=D
 report
 do_uvcatSD
 do_uvflag vis=sddata
 do_reduceSD 

You can replace the last line by

 do_reduceSD device=/null sleep=0

if you don't want do_reduceSD to prompt and display the data. The maps for each antenna are stored in SD/, and the pictures of all the 23 antennas for each molecule are stored in /. (e.g HCN.allants.gif)

If you want to just blanket remove an antenna from the maps, and discard it (this would be on top of the standard flagging) add badants, e.g.

 do_reduceSD  badants=7,23

but if you do, make sure this is saved in $MIS for others to pick up

 pipesave
 mis -i

Working from home/laptop

There's a potential pitfall if you want to work from home or your laptop, since you may not have mounted the rawdata directory (although you can actually do this using fusefs). But getdata now has an scp option, where you can full fake being at work, except of course symlinks don't work and you get a full copy of the data. Depending on your internet speed, this could be a slow processing getting the data. Here's an example:

 mkdir D1
 cd D1
 pipepar -c
 getdata trial=1 ary=D scp=teuben@chara.astro.umd.edu

this will ensure that your rawdata= is properly pointing to the motherland. If not, the mis -i would save a bad value to CVS and could mess up your collegues.

Nightly Script

A script is supposed to run regularly/nightly, where all calibrated and processed visibilities and single dish cubes should be found for any subsequent mapping experiments. The script lives in $MIS/templates/n1333_nightly.csh and can be easily adapted for your needs. If you place a symlink from your $MIS/Nightly to the location where we keep this Nightly, others can reuse the data. This is currently /n/chara6/teuben/n1333/Nightly_latest. You can find a more complete description in Raw & Calibrated Data